Sequence belongs on the specimen, not on a separate island.
APHL and WHO both treat genomics as core public-health capacity. Salus ties those pipelines to accession, coding, and human-gated reporting.
Clinical NGS next to the accession
Metagenomic and targeted NGS stay on the specimen. Organism calls get SNOMED when identified. Pipeline version is part of the method, not a side laptop.
AMR markers
blaKPC, blaNDM, mecA and the rest of the catalog pack report as Detected/Not detected plus the organism. Isolate submission notes stay on the card.
Wastewater and genomic epidemiology
Community signals are labeled as surveillance, never as a patient result. Lineage context can inform a surge pack without becoming an ELR.
PulseNet / outbreak linkage
The hub records that a sequence was generated and where it went. It does not replace the national PulseNet workflow. It stops the FASTQ from living only in email.
WHO and IHR-relevant threats
H5, viral hemorrhagic fevers, and other IHR events carry notification notes so a director sees the international obligation next to the state one.
What this is not
Salus does not claim to assemble Nanopore or Illumina reads inside the marketing site. Orchestration and lineage calling run in the jurisdiction tenant, under CLIA validation, with a human on release.
How Salus Agentic interfaces with bioinformatics
We maintain strict separation of concerns. We do not attempt to run supercomputing read assemblers inside a database application. We provide the public health LIMS of record that ingests pipeline results, binds them to the accession, and automates CDC reporting.
Bench Sequencer & Raw Reads
Physical sequencers (Illumina NextSeq/MiSeq, Oxford Nanopore, PacBio) execute sequencing chemistry and generate raw basecall files (.fastq.gz).
Bioinformatics Pipeline
Workflows (Nextflow, nf-core, Snakemake, Terra) execute quality trimming, de novo assembly (SPAdes/Unicycler), variant calling, and lineage prediction.
Metric Ingest API
Pipeline pushes a structured run summary via REST API directly to the jurisdiction's Salus Agentic instance, eliminating manual spreadsheet entry.
Salus Agentic LIMS of Record
Binds metrics to the accession, evaluates Westgard quality control gates, maps SNOMED/LOINC codes, and generates CDC PulseNet/CaliciNet/ARLN feeds under human sign-off.
Separation of concerns: Bioinformatics pipeline vs. Public health LIMS
| Functional Layer | Bioinformatics Pipeline (HPC / Cloud) | Salus Agentic (Public Health LIMS) |
|---|---|---|
| Primary Mission | Heavy graph mathematics, basecalling, read alignment, and de novo genome assembly | CLIA chain of custody, accessioning, quality control gates, and multi-destination surveillance reporting |
| Execution Environment | High-performance compute (HPC) cluster, Linux servers, AWS Batch, or Terra/Galaxy | Secure public health database, web-based laboratory desk, and standards-compliant API gateway |
| Data Handled | Gigabytes of raw nucleotide reads (FASTQ), alignments (BAM), and variation matrices (VCF) | Specimen accessions, clinical context, run QC metrics (Q30, depth), AMR resistance genes, and lineage calls |
| Regulatory Role | Bioinformatic pipeline versioning and analytic algorithm validation | Software of record for CLIA survey, laboratory director release, and patient privacy compliance |
| Public Health Reporting | Generates isolate assembly files and allele profiles for specialized repositories | Automated CDC PulseNet, CaliciNet, ARLN, state ELR (HL7 v2.5.1 / FHIR), and CDC NNDSS MMG feeds |
Why in-LIMS assembly fails state procurements
Read our technical explainer on physical sequencers, bioinformatic assemblers, and how clean JSON metric ingestion protects state CDC grant funding.
Turnkey manifests for national public health repositories
State epidemiologists and laboratory directors do not need to build custom export scripts. Salus Agentic generates validated, one-click submission packages for every major federal surveillance program.
Salmonella, E. coli, Listeria, Campylobacter
Automated BioNumerics upload manifests, run QC metrics (Q30, mean depth), and isolate metadata for rapid cluster detection.
Norovirus (GI/GII), Sapovirus
Standardized dual typing manifests capturing VP1 capsid and RdRp polymerase genotype designations for outbreak surveillance.
CRE, CRPA, CRAB, Candida auris
ARLN surveillance packages containing phenotypic AST breakpoints, carbapenemase genes (KPC, NDM, OXA, VIM), and isolate tracking.
State Notifiable Conditions
Turnkey HL7 v2.5.1 Message Mapping Guide (MMG) case notification segments linking laboratory accessions directly to NEDSS/EDSS.
Pathogen BioProjects & BioSamples
Compliant SRA XML and TSV submission packages associating demultiplexed FASTQ checksums with public health biosample accessions.
Influenza A/B (including H5N1), SARS-CoV-2
EpiFlu and EpiCoV batch submission manifests matching consensus FASTA sequences to clinical collection dates and geographic origins.
Start from the living cards
The catalog already carries IHR and surveillance notes. Native bioinformatic orchestration is a jurisdiction-tenant job under CLIA, listed honestly as a deepening module.